The one downside to simply invoking recovery mode when the star is lost, is that if recovery mode lasts 30+ minutes, the amount of drift might need a new slew, center and auto focus routine before restarting auto guiding.
I don't have a good feel for how often it clouds up only to clear again shortly thereafter. For now, I will use recovery mode options to simply end the sequence after 10 minutes of star lost. If its been gone for 10 minutes, it's probably a deteriorating night anyway. As far as windy, I can use the option to throw away the subs with large guiding deviations -- all you loose are some frames you would not have gotten if you shut down anyway.
In some future release, it might be useful to have an "OnRecovery()" function that could specify what you would like to do before restarting the subs. I can understand someone not wanting to lose an entire night when there are some brief clouds at 9PM.
Charlie